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Gas-phase conformations of the sodium-cationized forms of the 2'-deoxycytidine and cytidine mononucleotides, [pdCyd+Na] + and [pCyd+Na] + , are examined by infrared multiple photon dissociation action spectroscopy. Complimentary electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory provide candidate conformations and their respective predicted IR spectra for comparison across the IR fingerprint and hydrogen-stretching regions. Comparisons of the predicted IR spectra and the measured infrared multiple photon dissociation action spectra provide insight into the impact of sodium cationization on intrinsic mononucleotide structure. Further, comparison of present results with those reported for the sodium-cationized cytidine nucleoside analogues elucidates the impact of the phosphate moiety on gas-phase structure. Across the neutral, protonated, and sodium-cationized cytidine mononucleotides, a preference for stabilization of the phosphate moiety and nucleobase orientation is observed, although the details of this stabilization differ with the state of cationization. Several low-energy conformations of [pdCyd+Na] + and [pCyd+Na] + involving several different orientations of the phosphate moiety and sugar puckering modes are observed experimentally.

The molecular family of nucleotide triphosphates (NTPs), with adenosine 5'-triphosphate (ATP) as its best-known member, is of high biochemical importance as their phosphodiester bonds form Nature's main means to store and transport energy. Here, gas-phase IR spectroscopic studies and supporting theoretical studies have been performed on adenosine 5'-triphosphate, cytosine 5'-triphosphate and guanosine 5'-triphosphate to elucidate the intrinsic structural properties of NTPs, focusing on the influence of the nucleobase and the extent of deprotonation. Mass spectrometric studies involving collision induced dissociation showed similar fragmentation channels for the three studied NTPs within a selected charge state. The doubly charged anions exhibit fragmentation similar to the energy-releasing hydrolysis reaction in nature, while the singly charged anions show different dominant fragmentation channels, suggesting that the charge state plays a significant role in the favorability of the hydrolysis reaction. A combination of infrared ion spectroscopy and quantum-chemical computations indicates that the singly charged anions of all NTPs are preferentially deprotonated at their β-phosphates, while the doubly-charged anions are dominantly αβ-deprotonated. The assigned three-dimensional structure differs for ATP and CTP on the one hand and GTP on the other, in the sense that ATP and CTP show no interaction between nucleobase and phosphate tail, while in GTP they are hydrogen bonded. This can be rationalized by considering the structure and geometry of the NTPs where the final three dimensional structure depends on a subtle balance between hydrogen bond strength, flexibility and steric hindrance.

The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu] + and [Ura+Ag] + , were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra were measured over the IR fingerprint and hydrogen-stretching regions. Structures and linear IR spectra of the stable tautomeric conformations of these complexes were initially determined at the B3LYP/6-31G(d) level. The four most stable structures computed were also examined at the B3LYP/def2-TZVPPD level to improve the accuracy of the predicted IR spectra. Two very favorable modes of binding are found for [Ura+Cu] + and [Ura+Ag] + that involve O2N3 bidentate binding to the 2-keto-4-hydroxy minor tautomer and O4 monodentate binding to the canonical 2,4-diketo tautomer of Ura. Comparisons between the measured IRMPD and calculated IR spectra enable elucidation of the conformers present in the experiments. These comparisons indicate that both favorable binding modes are represented in the experimental tautomeric conformations of [Ura+Cu] + and [Ura+Ag] + . B3LYP suggests that Cu + exhibits a slight preference for O4 binding, whereas Ag + exhibits a slight preference for O2N3 binding. In contrast, MP2 suggests that both Cu + and Ag + exhibit a more significant preference for O2N3 binding. The relative band intensities suggest that O4 binding conformers comprise a larger portion of the population for [Ura+Ag] + than [Ura+Cu] + . The dissociation behavior and relative stabilities of the [Ura+M] + complexes, M + = Cu + , Ag + , H + , and Na + ) are examined via energy-resolved collision-induced dissociation experiments. The IRMPD spectra, dissociation behaviors, and binding preferences of Cu + and Ag + are compared with previous and present results for those of H + and Na + . Graphical Abstract ᅟ.

The gas-phase infrared multiple-photon dissociation and detachment (IRMPD) vibrational action spectra of the unsubstituted phenoxide anion and a series of fluorine- and trifluoromethyl-substituted phenoxide anions in the spectral region between 600 and 1800 cm(-1) are presented along with density functional theory (DFT) harmonic vibrational frequency calculations to establish the characteristic vibrations of the phenoxide functionality. The fluorophenoxide anions studied include the conjugate bases of o-, m-, and p-fluorophenol (C6H4FO(-)) as well as o-, m-, and p-α,α,α-trifluorocresol (CF3C6H4O(-)). The influence of the substituent on the characteristic vibrational frequencies is interpreted in terms of inductive and resonance shifts. In addition to the dissociation induced by infrared multiple-photon excitation, the electron detachment is also shown to play an important role in the decomposition of the unsubstituted phenoxide. It is demonstrated that the amount of electron detachment relative to dissociation is strongly mitigated by fluorination, and interpretations aided by DFT energy calculations suggest this is primarily due to the increased availability of low-energy dissociation pathways in the substituted phenoxides. Collision-induced dissociation (CID) mass spectrometry of the parent ions is used to estimate relative energies of the dissociation processes, and particular fragmentation motifs are elucidated. In particular, overall HF and CO losses provide facile decomposition pathways, yielding interesting fragment ions such as C6H(-) or C3H2FO(-) from the CF3C6H4O(-) parent anions.

Rationale: Hydroxamates are essential growth factors for some microbes, acting primarily as siderophores that solubilize iron for transport into a cell. Here we determined the intrinsic structure of 1:1 complexes between Boc-protected hydroxylamine and group I ([M(L)](+)) and group II ([M(L-H)](+)) cations, where M and L are the cation and ligand, respectively, which are convenient models for the functional unit of hydroxamate siderphores., Methods: The relevant complex ions were generated by electrospray ionization (ESI) and isolated and stored in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Infrared spectra of the isolated complexes were collected by monitoring (infrared) photodissociation yield as a function of photon energy. Experimental spectra were then compared to those predicted by density functional theory (DFT) calculations., Results: The infrared multiple photon dissociation (IRMPD) spectra collected are in good agreement with those predicted to be lowest-energy by DFT. The spectra for the group I complexes contain six resolved absorptions that can be attributed to amide I and II type and hydroxylamine N-OH vibrations. Similar absorptions are observed for the group II cation complexes, with shifts of the amide I and amide II vibrations due to the change in structure with deprotonation of the hydroxylamine group., Conclusions: IRMPD spectroscopy unequivocally shows that the intrinsic binding mode for the group I cations involves the O atoms of the amide carbonyl and hydroxylamine groups of Boc-hydroxylamine. A similar binding mode is preferred for the group II cations, except that in this case the metal ion is coordinated by the O atom of the deprotonated hydroxylamine group., (Copyright © 2013 John Wiley & Sons, Ltd.)

We report the direct angle-resolved measurement of collision-induced alignment of short-lived electronically excited molecules using crossed atomic and molecular beams. Utilizing velocity-mapped ion imaging, we measure the alignment of NO in its first electronically excited state (A(2)Σ(+)) following single collisions with Ne atoms. We prepare A(2)Σ(+) (v = 0, N = 0, j = 0.5) and by comparing images obtained using orthogonal linear probe laser polarizations, we experimentally determine the degree of alignment induced by collisional rotational excitation for the final rotational states N' = 4, 5, 7, and 9. The experimental results are compared to theoretical predictions using both a simple classical hard-shell model and quantum scattering calculations on an ab initio potential energy surface (PES). The experimental results show overall trends in the scattering-angle dependent polarization sensitivity that are accounted for by the simple classical model, but structure in the scattering-angle dependence that is not. The quantum scattering calculations qualitatively reproduce this structure, and we demonstrate that the experimental measurements have the sensitivity to critique the best available potential surfaces. This sensitivity to the PES is in contrast to that predicted for ground-state NO(X) alignment.

In this work, we regiospecifically generate and compare the gas-phase properties of two isomeric forms of tryptophan radical cations-a distonic indolyl N-radical (H3N(+) - TrpN(•)) and a canonical aromatic π (Trp(•+)) radical cation. The distonic radical cation was generated by nitrosylating the indole nitrogen of tryptophan in solution followed by collision-induced dissociation (CID) of the resulting protonated N-nitroso tryptophan. The π-radical cation was produced via CID of the ternary [Cu(II)(terpy)(Trp)](•2+) complex. CID spectra of the two isomeric species were found to be very different, suggesting no interconversion between the isomers. In gas-phase ion-molecule reactions, the distonic radical cation was unreactive towards n-propylsulfide, whereas the π radical cation reacted by hydrogen atom abstraction. DFT calculations revealed that the distonic indolyl radical cation is about 82 kJ/mol higher in energy than the π radical cation of tryptophan. The low reactivity of the distonic nitrogen radical cation was explained by spin delocalization of the radical over the aromatic ring and the remote, localized charge (at the amino nitrogen). The lack of interconversion between the isomers under both trapping and CID conditions was explained by the high rearrangement barrier of ca.137 kJ/mol. Finally, the two isomers were characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy in the ~1000-1800 cm(-1) region. It was found that some of the main experimental IR features overlap between the two species, making their distinction by IRMPD spectroscopy in this region problematic. In addition, DFT theoretical calculations showed that the IR spectra are strongly conformation-dependent.

The gas phase structures of the deprotonated 2'-deoxymononucleotides including 2'-deoxyadenosine-5'-monophosphate (dA5'p), 2'-deoxycytidine-5'-monophosphate (dC5'p), 2'-deoxyguanosine-5'-monophosphate (dG5'p), and thymidine-5'-monophosphate (T5'p) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The measured IRMPD action spectra of all four deprotonated DNA mononucleotides exhibit unique spectral features in the region extending from ~600 to 1800 cm(-1) such that they can be readily differentiated from one another. The measured IRMPD action spectra are compared to the linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformations of these species accessed in the experiments. On the basis of these comparisons and the computed energetic information, the most stable conformations of the deprotonated forms of dA5'p, dC5'p, and T5'p are conformers where the ribose moiety adopts a C3' endo conformation and the nucleobase is in an anti conformation. By contrast, the most stable conformations of the deprotonated form of dG5'p are conformers where the ribose adapts a C3' endo conformation and the nucleobase is in a syn conformation. In addition to the ground-state conformers, several stable low-energy excited conformers that differ slightly in the orientation of the phosphate ester moiety were also accessed in the experiments.

Ion-neutral complexes of pentaalalanine with several singly- and doubly charged metal ions are examined using conformation analysis by infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) computations. The infrared spectroscopy in the 1500-1800 cm(-1) region is found to be conformationally informative; in particular, the frequency of the C═O stretching mode of the terminal carboxyl group is diagnostic for hydrogen bonding of the terminal hydroxyl. The doubly charged alkaline earth metal ions (Ca(2+) and Ba(2+)) enforce a highly structured chelation shell around the metal ion, with six strongly bound Lewis-basic chelation sites, and no hydroxyl hydrogen bonding. With the more weakly binding alkali metal ions (Na(+), K(+), and Cs(+)), structures with intramolecular hydrogen bonds are more favorable, leading to dominance of conformations with lower degrees of metal ion chelation. The favored coordination mode correlates with ionic charge and binding strength but is not related to the ionic radius of the metal ion.

The conjugate base of para-coumaric acid, which can be conveniently generated in the gas phase by electrospray ionization (ESI), is a commonly used model system for the chromophore of the photoactive yellow protein. Here we report its gas-phase IR spectrum, which shows that the anion easily adopts a carboxylate structure lying 60 kJ/mol higher in energy than the global minimum phenoxide structure. Generation of the biologically more relevant phenoxide isomer by ESI can be achieved using dry acetonitrile as solvent.

In an effort to understand the chemical factors that stabilize dianions, experimental and theoretical studies on the stability of the tartrate dianion were performed. Quantum chemical calculations at the coupled cluster level reveal only a metastable state with a possible decomposition pathway (O(2)C-CH(OH)-CH(OH)-CO(2))(2-) → (O(2)C-CH(OH)-CH(OH))(•-) + CO(2) + e(-) explaining the observed gas-phase instability of this dianion. Further theoretical data were collected for the bare dianion, this molecule complexed to water, sodium, and a proton, in both the meso and l forms as well as for the uncomplexed radical anion and neutral diradical. The calculations suggest that the l-tartrate dianion is more thermodynamically stable than the dianion of the meso stereoisomer and that either dianion can be further stabilized by association with a separate species that can help to balance the charge of the molecular complex. Mass spectrometry was then used to measure the energy needed to initiate collisionally induced dissociation of the racemic tartrate dianion and for the proton and sodium adducts of both the racemic and meso form of this molecule. Infrared action spectra of the dianion stereoisomers complexed with sodium were also acquired to determine the influence of the metal ion on the vibrations of the dianions and validate the computationally predicted structures. These experimental data support the theoretical conclusions and highlight the instability of the bare tartrate dianion. From the experimental work, it could also be concluded that the pathway leading to dissociation is under kinetic control because the sodium adduct of the racemic stereoisomer dissociated at lower collisional energy, although it was calculated to be more stable, and that decomposition proceeded via C-C bond dissociation as computationally predicted. Taken together, these data provide insight into the gas-phase stability of the tartrate dianion and highlight the role of adducts in stabilizing this species.

The elucidation of the structural requirements for molecular recognition by the crown ether (18-crown-6)-2,3,11,12-tetracarboxylic acid (18c6H(4)) and its cationic complexes constitutes a topic of current fundamental and practical interest in catalysis and analytical sciences. The flexibility of the central ether ring and its four carboxyl side arms poses important challenges to experimental and theoretical approaches. In this study, infrared action vibrational spectroscopy and quantum mechanical computations are employed to characterize the conformational structure of the isolated gas phase complex formed by the 18c6H(4) host with NH(4)(+) as guest. The results show that the most stable gas-phase structure is a barrel-like conformation sustained by tetrapodal H-bonding of the ammonia cation with two C=O side groups and with four oxygen atoms of the ether ring in a bifurcated arrangement. Interestingly, a similar structure had been proposed in previous crystallographic studies. The experiment also provides evidence for a significant contribution of a higher energy bowl-like conformer with features resembling those adopted by 18c6H(4) in the analogous complexes with secondary amines. Such a conformation displays H-bonding between confronted side carboxyl groups and tetrapodal binding of the NH(4)(+) with the ether ring and with one C=O group. Structures involving even more extensive intramolecular H-bonding in the 18c6H(4) substrate are found to lie higher in energy and are ruled out by the experiment., (© 2012 American Institute of Physics)

The gas phase structures of cationized histidine (His), including complexes with Li(+), Na(+), K(+), Rb(+), and Cs(+), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser, in conjunction with quantum chemical calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) (Li(+), Na(+), and K(+) complexes) and B3LYP/HW*/6-311+G(d,p) (Rb(+) and Cs(+) complexes) levels of theory, where HW* indicates that the Hay-Wadt effective core potential with additional polarization functions was used on the metals. Single point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. On the basis of these experiments and calculations, the only conformation that reproduces the IRMPD action spectra for the complexes of the smaller alkali metal cations, Li(+)(His) and Na(+)(His), is a charge-solvated, tridentate structure where the metal cation binds to the backbone carbonyl oxygen, backbone amino nitrogen, and nitrogen atom of the imidazole side chain, [CO,N(α),N(1)], in agreement with the predicted ground states of these complexes. Spectra of the larger alkali metal cation complexes, K(+)(His), Rb(+)(His), and Cs(+)(His), have very similar spectral features that are considerably more complex than the IRMPD spectra of Li(+)(His) and Na(+)(His). For these complexes, the bidentate [CO,N(1)] conformer in which the metal cation binds to the backbone carbonyl oxygen and nitrogen atom of the imidazole side chain is a dominant contributor, although features associated with the tridentate [CO,N(α),N(1)] conformer remain, and those for the [COOH] conformer are also clearly present. Theoretical results for Rb(+)(His) and Cs(+)(His) indicate that both [CO,N(1)] and [COOH] conformers are low-energy structures, with different levels of theory predicting different ground conformers.

All eight D-aldohexoses and aldohexoses derived from the non-reducing end of disaccharides were investigated by variable-wavelength infrared multiple-photon dissociation (IRMPD) as anions in the negative-ion mode. Spectroscopic evidence supports the existence of a relatively abundant open-chain configuration of the anions in the gas phase, based on the observation of a significant carbonyl absorption band near 1710 cm(-1). The abundance of the open-chain configuration of the aldohexose anions was approximately 1000-fold or greater than that of the neutral sugars in aqueous solution. This provides an explanation as to why it has not been possible to discriminate the anomeric configuration of aldohexose anions in the gas phase when derived from the non-reducing sugar of a disaccharide. Evidence from photodissociation spectra also indicates that the different aldohexoses yield product ions with maximal abundances at different wavelengths, and that the carbonyl stretch region is useful for differentiation of sugar stereochemistries. Quantum-chemical calculations indicate relatively low energy barriers to intramolecular proton transfer between hydroxyl groups and adjacent alkoxy sites located on open-chain sugar anions, suggesting that an ensemble of alkoxy charge locations contributes to their observed photodissociation spectra. Ring opening of monosaccharide anions and interconversion among configurations is an inherent property of the ions themselves and occurs in vacuo independent of solvent participation., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Infrared multiple photon dissociation spectroscopy and hydrogen/deuterium exchange methods are used to confirm the macrocylic structure of a b(6) peptide fragment by direct comparison with a synthetically made cyclic peptide. The acetylation of the peptide N-terminus results in the inhibition of the macrocyclic formation, supporting the "head-to-tail" cyclization mechanism. Differences in hydrogen/deuterium exchange rates for macrocyclic and oxazalone structure peptide fragments are interpreted to be a result of the complex interplay of multiple basic sites in the peptide fragment, supporting the relay mechanism for deuterium exchange with CH(3)OD., (Copyright © 2011 John Wiley & Sons, Ltd.)

Fluorescein (FL) and its derivative 2',7'-dichlorofluoroescein (DCF) are well-known fluorescent dyes used in many biological and biochemical applications. Although extensive studies have been carried out to investigate their chemical and photophysical properties in different solvent media, little is known about their intrinsic behaviors in the gas phase. Here, infrared multiple photon dissociation (IRMPD) action spectra are reported for the three charged prototropic forms of FL and DCF and compared with computed IR spectra from electronic structure calculations. In each case, the measured spectra show good agreement with the calculated spectra of the lowest energy computed conformer. Moreover, the major bands of the monoanion IRMPD spectra show striking similarities to those of the dianions and are quite different from those of the cations. These experimental results clearly indicate that the gaseous monoanions are predominantly deprotonated on the xanthene chromophore, rather than the benzoate deprotonation site favored in solution. Investigations such as this, which provide a better understanding of intrinsic properties of ionic dyes, forms a baseline from which to elucidate solvent effects and will aid the rational design of dyes possessing desirable fluorescence properties., (© 2011 American Chemical Society)

Ion trap tandem mass spectrometry with collision-induced dissociation, and the combination of infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations, were used to characterize singly charged, 1:1 complexes of Ca(2+), Sr(2+) and Ba(2+) with salicylate. For each metal-salicylate complex, the CID pathways are: (a) elimination of CO(2) and (b) formation of [MOH](+) where M = Ca(2+), Sr(2+) or Ba(2+). DFT calculations predict three minima for the cation-salicylate complexes which differ in the mode of metal binding. In the first, the metal ion is coordinated by O atoms of the (neutral) phenol and carboxylate groups of salicylate. In the second, the cation is coordinated by phenoxide and (neutral) carboxylic acid groups. The third mode involves coordination by the carboxylate group alone. The infrared spectrum for the metal-salicylate complexes contains a number of absorptions between 1000 and 1650 cm(-1), and the best correlation between theoretical and experimental spectra is found for the structure that features coordination of the metal ion by phenoxide and the carbonyl O of the carboxylic acid group, consistent with the calculated energies for the respective species., (Copyright © 2011 John Wiley & Sons, Ltd.)

The complexes formed by crown ethers with hydronium and ammonium cations are of key relevance for the understanding of their supramolecular behavior in protic solvents. In this work, the complexes of the 15-crown-5 (15c5) and 18-crown-6 (18c6) ethers with H₃O⁺ and NH₄⁺ and their deuterated variants are investigated under isolated conditions. The study employs infrared multiple photon dissociation (IRMPD) vibrational spectroscopy and DFT B3LYP/6-31++G(d,p) calculations for conformational assignment. The 18c6 ether provides two energetically nearby C(3v) conformations with commensurate linear O-H···O and N-H···O bonds. The 15c5 ether ring adopts partially folded asymmetric pyramidal geometries, yielding one shorter linear H bond and two longer non-linear H bonds. Remarkably, an appreciable broadening of the IRMPD vibrational bands is observed for the 15c5-H₃O⁺/D₃O⁺ complexes. This can be interpreted as a signature for partial sharing of the proton (or deuteron) between the water and the crown ether along the linear O-H···O intermolecular H bond, which is indeed particularly short for this complex.

Structures and binding thermochemistry are investigated for protonated PhePhe and for complexes of PhePhe with the alkaline-earth ions Ba(2+) and Ca(2+), the alkali-metal ions Li(+), Na(+), K(+), and Cs(+), and the transition-metal ion Ag(+). The two neighboring aromatic side chains open the possibility of a novel encapsulation motif of the metal ion in a double cation-π configuration, which is found to be realized for the alkaline-earth complexes and, in a variant form, for the Ag(+) complex. Experimentally, complexes are formed by electrospray ionization, trapped in an FT-ICR mass spectrometer, and characterized by infrared multiple photon dissociation (IRMPD) spectroscopy using the free electron laser FELIX. Interpretation is assisted by thermochemical and IR spectral calculations using density functional theory (DFT). The IRMPD spectrum of protonated PhePhe is reproduced with good fidelity by the calculated spectrum of the most stable conformation, although the additional presence of the secondmost stable conformation is not excluded. All metal-ion complexes have charge-solvated binding modes, with zwitterion (salt bridge) forms being much less stable. The amide oxygen always coordinates to the metal ion, as well as at least one phenyl ring (cation-π interaction). At least one additional chelation site is always occupied, which may be either the amino nitrogen or the carboxy carbonyl oxygen. The alkaline-earth complexes prefer a highly compact caged structure with both phenyl rings providing cation-π stabilization in a "sandwich" configuration (OORR chelation). The alkali-metal complexes prefer open-cage structures with only one cation-π interaction, except perhaps Cs(+). The Ag(+) complex shows a unique preference for the closed-cage amino-bound NORR structure. Ligand-driven perturbations of normal-mode frequencies are generally found to correlate linearly with metal-ion binding energy.

The gas-phase structures of transition-metal dication (Zn(2+) and Cd(2+)) complexes with varying sized crown ethers, 12-crown-4 (12c4), 15-crown-5 (15c5), and 18-crown-6 (18c6), are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and quantum mechanical calculations. The measured spectra span the 750-1600 cm(-1) infrared range, utilizing light generated by a free electron laser, and are compared to predicted spectra calculated at the B3LYP/6-311+G(d,p) or B3LYP/Def2TZVP levels of theory. Spectra with the largest and most flexible crown ether, 18c6, indicate that the crown is highly distorted, wrapping in a tight cage-like structure around both dications studied. The 15c5 adopts a folded orientation for the Zn(2+) complex yet is almost planar when complexed with the larger Cd(2+) ion. The Zn(2+)(12c4) spectrum has bands appearing at lower frequencies than the other systems, consistent with an open conformation such that the metal is exposed, lying above the center of mass of the crown ether ring. The open structures of the Zn(2+)(12c4) and Cd(2+)(15c5) complexes have implications for solvent interactions in the condensed phase. The conformation of each metal-crown complex is highly dependent on metal size, charge, and crown ether flexibility, such that a delicate balance of minimizing the metal-oxygen bond lengths but maximizing the oxygen-oxygen distances arises. These competing influences are reflected in both the spectra and lowest-energy conformations., (© 2011 American Chemical Society)

Infrared multiple photon dissociation (IRMPD) was used to generate vibrational spectra of ions produced with a direct analysis in real time (DART) ionization source coupled to a 4.7 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The location of protonation on the nerve agent simulants diisopropyl methylphosphonate (DIMP) and dimethyl methylphosphonate (DMMP) was studied while solutions of the compounds were introduced for extended periods of time with a syringe pump. Theoretical vibrational spectra were generated with density functional theory calculations. Visual comparison of experimental mid-IR IRMPD spectra and theoretical spectra could not establish definitively if a single structure or a mixture of conformations was present for the protonated parent of each compound. However, theoretical calculations, near-ir IRMPD spectra, and frequency-to-frequency and statistical comparisons indicated that the protonation site for both DIMP and DMMP was predominantly, if not exclusively, the phosphonyl oxygen instead of one of the oxygen atoms with only single bonds.

Structural characterization of protonated gas-phase ions of cysteine and dopamine by infrared multiple photon dissociation (IRMPD) spectroscopy using a free electron laser in combination with theory based on DFT calculations reveals the presence of two types of protonated dimer ions in the electrospray mass spectra of the metabolites. In addition to the proton-bound dimer of each species, the covalently bound dimer of cysteine (bound by a disulfide linkage) has been identified. The dimer ion of m/z 241 observed in the electrospray mass spectra of cysteine has been identified as protonated cystine by comparison of the experimental IRMPD spectrum to the IR absorption spectra predicted by theory and the IRMPD spectrum of a standard. Formation of the protonated covalently bound disulfide-linked dimer ions (i.e. protonated cystine) from electrospray of cysteine solution is consistent with the redox properties of cysteine. Both the IRMPD spectra and theory indicate that in protonated cystine the covalent disulfide bond is retained and the proton is involved in intramolecular hydrogen bonding between the amine groups of the two cysteine amino acid units. For cysteine, the protonated covalently bound dimer (m/z 241) dominated the mass spectrum relative to the proton-bound dimer (m/z 243), but this was not the case for dopamine, where the protonated monomer and the proton-bound dimer were both observed as major ions. An extended conformation of the ethylammonium side chain of gas-phase protonated dopamine monomer was verified from the correlation between the predicted IR absorption spectra and the experimental IRMPD spectrum. Dopamine has the same extended ethylamine side chain conformation in the proton-bound dopamine dimer identified in the mass spectra of electrosprayed dopamine. The structure of the proton-bound dimer of dopamine is confirmed by calculations and the presence of an IR band due to the shared proton. The presence of the shared proton in the protonated cystine ion can be inferred from the IRMPD spectrum.

Chirality reversal of a residue in a peptide can change its mode of binding to a metal ion, as shown here experimentally by gas-phase IR spectroscopy of peptide-metal ion complexes. The binding conformations of Li(+), Na(+), and H(+) with the LL and DL stereoisomers of PhePhe were compared through IR ion spectroscopy using the FELIX free-electron laser. For the DL isomer, both Li(+) and Na(+) exclusively coordinate to the amide O atom, the carboxyl O atom, and one of the aromatic rings (the OOR conformation), while for the LL isomer, a mixture of the OOR and NOR conformations was found. The stereochemically induced change in conformation is shown to reflect the strength of an NH···π interaction remote from the metal ion site. Protonated PhePhe shows no stereochemically induced variation in binding geometry.

The gas-phase infrared spectra of radical cationic and protonated corannulene were recorded by infrared multiple-photon dissociation (IRMPD) spectroscopy using the IR free electron laser for infrared experiments. Electrospray ionization was used to generate protonated corannulene and an IRMPD spectrum was recorded in a Fourier-transform ion cyclotron resonance mass spectrometer monitoring H-loss as a function of IR frequency. The radical cation was produced by 193-nm UV photoionization of the vapor of corannulene in a 3D quadrupole trap and IR irradiation produces H, H(2), and C(2)H(x) losses. Summing the spectral response of the three fragmentation channels yields the IRMPD spectrum of the radical cation. The spectra were analyzed with the aid of quantum-chemical calculations carried out at various levels of theory. The good agreement of theoretical and experimental spectra for protonated corannulene indicates that protonation occurs on one of the peripheral C-atoms, forming an sp(3) hybridized carbon. The spectrum of the radical cation was examined taking into account distortions of the C(5v) geometry induced by the Jahn-Teller effect as a consequence of the degenerate (2)E(1) ground electronic state. As indicated by the calculations, the five equivalent C(s) minima are separated by marginal barriers, giving rise to a dynamically distorted system. Although in general the character of the various computed vibrational bands appears to be in order, only a qualitative match to the experimental spectrum is found. Along with a general redshift of the calculated frequencies, the IR intensities of modes in the 1000-1250 cm(-1) region show the largest discrepancy with the harmonic predictions. In addition to CH "in-plane" bending vibrations, these modes also exhibit substantial deformation of the pentagonal inner ring, which may relate directly to the vibronic interaction in the radical cation.

The structure and reactivity of the cysteine methyl ester radical cation, CysOMe(.+) , have been examined in the gas phase using a combination of experiment and density functional theory (DFT) calculations. CysOMe(.+) undergoes rapid ion-molecule reactions with dimethyl disulfide, allyl bromide, and allyl iodide, but is unreactive towards allyl chloride. These reactions proceed by radical atom or group transfer and are consistent with CysOMe(.+) possessing structure 1, in which the radical site is located on the sulfur atom and the amino group is protonated. This contrasts with DFT calculations that predict a captodative structure 2, in which the radical site is positioned on the α carbon and the carbonyl group is protonated, and that is more stable than 1 by 13.0 kJ mol(-1) . To resolve this apparent discrepancy the gas-phase IR spectrum of CysOMe(.+) was experimentally determined and compared with the theoretically predicted IR spectra of a range of isomers. An excellent match was obtained for 1. DFT calculations highlight that although 1 is thermodynamically less stable than 2, it is kinetically stable with respect to rearrangement., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Electrospray ionization produces phenylalanine (Phe) complexes of the alkali metal ion series, plus Ag(+) and Ba(2+). Infrared multiple photon dissociation (IRMPD) spectroscopy using the FELIX free electron laser light source is used to characterize the conformations of the ions, in conjunction with density functional theory (DFT) calculations giving thermochemical information and computed infrared spectra for likely candidate conformations. For complexes of small, singly charged ions (Li(+), Na(+), K(+) and Ag(+)) a single tridentate, charge-solvated conformational theme (N/O/Ring) binding amino nitrogen, carbonyl oxygen and the aromatic ring to the metal ion accounts for all the observations. The larger alkalis Rb(+) and Cs(+) show clear spectroscopic evidence of mixed populations, containing substantial fractions of both tridentate and also bidentate chelation. For Rb(+) the bidentate fraction is assigned as the (O/Ring) chelation pattern, while for Cs(+) a mixture of (O/Ring) and (O/O) chelation patterns seems likely. All of the smaller ions with high positive charge density have a clear preference for cation-π interaction with the side-chain aromatic ring, but for the larger ions Rb(+) and particularly Cs(+) this interaction becomes sufficiently weak to allow conformations having the metal ion remote from the π system. The Ba(2+) complex is unique in showing clear evidence of a major fraction of salt-bridge (zwitterionic) ions along with charge-solvated conformations. Plots of the frequency shifts of the two highly perturbed ligand vibrational modes (C[double bond, length as m-dash]O stretch and NH(2) frustrated inversion) give good linear correlations with the binding energy of the metal to the ligand.

Action spectroscopy of gaseous Me(3)BF(-) and Me(2)BCH(2)(-), determined using IR multiple photon dissociation (IRMPD), exhibits experimental peak positions in good agreement with those predicted by anharmonic DFT calculations at the B3LYP/aug-cc-pVTZ level. Comparing spring constants among boron-carbon bonds and consideration of isoelectronic systems reveals that the anions have B-CH(3) bonds a factor of 1.3-1.4 weaker than those in neutral trimethylboron, suggesting a greater role for hyperconjugation in B(CH(3))(3) than inferred from previous vibrational spectroscopic studies.

The collision-induced dissociation (CID) products b(2)-b(4) from Leu-enkephalin are examined with infrared multiple-photon dissociation (IR-MPD) spectroscopy and gas-phase hydrogen/deuterium exchange (HDX). Infrared spectroscopy reveals that b(2) exclusively adopts oxazolone structures, protonated at the N-terminus and at the oxazolone ring N, based on the presence and absence of diagnostic infrared vibrations. This is correlated with the presence of a single HDX rate. For the larger b(3) and b(4), the IR-MPD measurements display diagnostic bands compatible with a mixture of oxazolone and macrocycle structures. This result is supported by HDX experiments, which show a bimodal distribution in the HDX spectra and two distinct rates in the HDX kinetic fitting. The kinetic fitting of the HDX data is employed to derive the relative abundances of macrocycle and oxazolone structures for b(3) and b(4), using a procedure recently implemented by our group for a series of oligoglycine b fragments (Chen et al. J. Am. Chem. Soc.2009, 131(51), 18272-18282. doi: 10.1021/ja9030837). In analogy to that study, the results suggest that the relative abundance of the macrocycle structure increases as a function of b fragment size, going from 0% for b(2) to approximately 6% for b(3), and culminating in 31% for b(4). Nonetheless, there are also surprising differences between both studies, both in the exchange kinetics and the propensity in forming macrocycle structures. This indicates that the chemistry of "head-to-tail" cyclization depends on subtle differences in the sequence as well as the size of the b fragment., (Copyright 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.)

Crown ethers provide a valuable benchmark for the comprehension of molecular recognition mediated by inclusion complexes. One of the most relevant crown ethers, 18-crown-6 (18c6), features a flexible six-oxygen cyclic backbone that is well-known for its selective cation binding. This study employs infrared spectroscopy and quantum mechanical calculations to elucidate the structure of the gas-phase complexes formed by the 18c6 ether with the alkali metal cations. It is shown that symmetric and chiral arrangements play a dominant role in the conformational landscape of the 18c6-alkali system. Most stable 18c6-M(+) conformers are found to have symmetries C(3v) and C(2) for Cs(+), D(3d) for K(+), C(1) and D(3d) for Na(+), and D(2) for Li(+). Remarkably, whereas the bare 18c6 ether is achiral, chirality emerges in the C(2) and D(2) 18c6-M(+) conformations, both of which involve pairs of stable atropoisomers capable of acting as enantiomeric selective substrates.

Triuret (also known as carbonyldiurea, dicarbamylurea, or 2,4-diimidotricarbonic diamide) is a byproduct of purine degradation in living organisms. An abundant triuret precursor is uric acid, whose level is altered in multiple metabolic pathologies. Triuret can be generated via urate oxidation by peroxynitrite, the latter being produced by the reaction of nitric oxide radical with superoxide radical anion. From this standpoint, an excess production of superoxide radical anions could indirectly favor triuret formation; however very little is known about the potential in vivo roles of this metabolite. Triuret's structure is suggestive of its ability to adopt various conformations and act as a flexible ligand for metal ions. In the current study, HPLC-MS/MS, energy-resolved mass spectrometry, selected ion monitoring, collision-induced dissociation, IRMPD spectroscopy, Fourier transform-ion cyclotron resonance mass spectrometry and computational methods were employed to characterize the structure of triuret and its metal complexes, to determine the triuret-alkali metal binding motif, and to evaluate triuret affinity toward alkali metal ions, as well as its affinity for Na(+) and K(+) relative to other organic ligands. The most favored binding motif was determined to be a bidentate chelation of triuret with the alkali metal cation involving two carbonyl oxygens. Using the complexation selectivity method, it was observed that in solution triuret has an increased affinity for potassium ions, compared to sodium and other alkali metal ions. We propose that triuret may act as a potential hypokalemic agent under pathophysiological conditions conducive to its excessive formation and thus contribute to electrolyte disorders. The collision- or photo-induced fragmentation channels of deprotonated and protonated triuret, as well as its alkali metal adducts, are likely to mimic the triuret degradation pathways in vivo., (2010 Elsevier Inc. All rights reserved.)

We present the first infrared spectra of a mass-selected deprotonated peptide anion (AlaAlaAla) and its decarboxylated fragment anion formed by collision induced dissociation. Spectra are obtained by IRMPD spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Spectra have been recorded over the 800-1800 cm(-1) spectral range and compared with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. These experiments suggest a carboxylate anion for [M-H](-) and an amide deprotonated (amidate) structure for the a(3) fragment anion [M-H-CO(2)](-). The frequency for the amidate carbonyl stretch occurring around 1555 +/- 5 cm(-1) has been confirmed by additional spectroscopic studies of the conjugated base of N-methylacetamide, which serves as a simple model system for the deprotonated amide linkage in a peptide anion., (Copyright 2010. Published by Elsevier Inc.)

Multiple-stage tandem mass spectrometry and collision-induced dissociation were used to investigate loss of H(2)O or CH(3)OH from protonated versions of GGGX (where X = G, A, and V), GGGGG, and the methyl esters of these peptides. In addition, wavelength-selective infrared multiple photon dissociation was used to characterize the [M + H - H(2)O](+) product derived from protonated GGGG and the major MS(3) fragment, [M + H - H(2)O - 29](+) of this peak. Consistent with the earlier work [ Ballard , K. D. ; Gaskell , S. J. J. Am. Soc. Mass Spectrom. 1993 , 4 , 477 - 481 ; Reid , G. E. ; Simpson , R. J. ; O'Hair , R. A. J. Int. J. Mass Spectrom. 1999 , 190/191 , 209 -230 ], CID experiments show that [M + H - H(2)O](+) is the dominant peak generated from both protonated GGGG and protonated GGGG-OMe. This strongly suggests that the loss of the H(2)O molecule occurs from a position other than the C-terminal free acid and that the product does not correspond to formation of the b(4) ion. Subsequent CID of [M + H - H(2)O](+) supports this proposal by resulting in a major product that is 29 mass units less than the precursor ion. This is consistent with loss of HN horizontal lineCH(2) rather than loss of carbon monoxide (28 mass units), which is characteristic of oxazolone-type b(n) ions. Comparison between experimental and theoretical infrared spectra for a group of possible structures confirms that the [M + H - H(2)O](+) peak is not a substituted oxazolone but instead suggests formation of an ion that features a five-membered ring along the peptide backbone, close to the amino terminus. Additionally, transition structure calculations and comparison of theoretical and experimental spectra of the [M + H - H(2)O - 29](+) peak also support this proposal.

The gas-phase structures of alkali-metal cation complexes of the amino acid methionine (Met) as well as protonated methionine are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser. Spectra of Li(+)(Met) and Na(+)(Met) are similar and relatively simple, whereas the spectra of K(+)(Met), Rb(+)(Met), and Cs(+)(Met) include distinctive new bands. Measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311+G(d,p) level of theory to identify the conformations present in the experimental studies. For Li(+) and Na(+) complexes, the only conformation present is a charge-solvated, tridentate structure that binds the metal cation to the amine and carbonyl groups of the amino acid backbone and the sulfur atom of the side chain, [N,CO,S]. In addition to the [N,CO,S] conformer, bands corresponding to alkali-metal cation binding to a bidentate zwitterionic structure, [CO(2)(-)], are clearly present for the K(+), Rb(+), and Cs(+) complexes. Theoretical calculations of the lowest energy conformations of Rb(+) and Cs(+) complexes suggest that the experimental spectra could also include contributions from two additional charge-solvated structures, tridentate [COOH,S] and bidentate [COOH]. For H(+)(Met), the IRMPD action spectrum is reproduced by multiple low-energy [N,CO,S] conformers, in which the protonated amine group hydrogen bonds to the carbonyl oxygen atom and the sulfur atom of the amino acid side chain. These [N,CO,S] conformers only differ in their side-chain orientations.

Collision-induced dissociation (CID), along with infrared multiple photon dissociation/detachment (IRMPD) techniques, is utilized to study a series of doubly substituted aromatic dianions containing sulfonate and carboxylate functionalities (1,2- and 1,3-benzenedisulfonate, 1,5-naphthalenedisulfonate, 2,6-naphthalenedisulfonate, 4-sulfobenzoate, 2,6-naphthalenedicarboxylate, and terephthalate dianions). The molecules were chosen because of the electronegativity of the CO(2) and SO(3) moieties along with their varied spatial separation in order to investigate the effect of the repulsive Coulomb barrier (RCB) on the dianions' respective dissociation pathways. Density functional theory calculations of the structures, electron detachment and dissociation energies, as well as vibrational frequencies are performed. Calculated infrared active vibrational frequencies are largely in agreement with the IRMPD spectra which provide support for interpretations based upon computed energies. Calculated and experimental results show that fragmentation dominates over electron detachment as the lowest energy dissociation pathway for these systems and the nature of this dissociation is dictated by properties of the substituent group. CID and IRMPD of dianions with two sulfonate groups (SO(3)(-)) resulted in a single dissociation channel leading to observation of SO(3)(-) and its anion conjugate pair, whereas the carboxylate (CO(2)(-)) containing dianions dissociated via loss of one or both CO(2) molecules and an electron. The SO(3)(-) collisional dissociation exhibited a clear energetic threshold toward ionic fragmentation with an isomeric dependence that is in reasonable agreement with a simple electrostatic model of the RCB, as well as with published reports on electron photodetachment. The loss of one or both CO(2) units and an electron from CID of the carboxylate dianions appeared with no threshold (dissociation occurs with no collision gas), implying these dianions to be metastable toward the dissociation pathway. However, calculations show these ions to be energetically stable toward dissociation as well as electron detachment. More importantly, in the case of the 2,6-naphthalenedicarboxylate dianion, experiments performed at the FELIX Fourier-transform ion cyclotron resonance facility and the ELISA electrostatic storage ring, where ions are collisionally cooled prior to analysis, showed this ion to be stable (tau>1.5 s). We conclude that the carboxylate (CO(2)(-)) containing dianions formed in the present CID experiment are electronically stable but vibrationally metastable due to internal energy imparted in the harsh electrospray conditions. The delocalized nature of the excess electrons associated with the carboxylate containing dianions may lead to circumvention of the RCB by dissociating via neutral fragmentation followed by (or accompanied by) electron detachment.

The structures of gas-phase, metal chlorate anions with the formula [M(ClO(3))(2)](-), M = Na and K, were determined using tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy. Structural assignments for both anions are based on comparisons of the experimental vibrational spectra for the two species with those predicted by density functional theory (DFT) and involve conformations that feature either bidentate or tridentate coordination of the cation by chlorate. Our results strongly suggest that a structure in which both chlorate anions are bidentate ligands is preferred for [Na(ClO(3))(2)](-). However, for [K(ClO(3))(2)](-) the best agreement between experimental and theoretical spectra is obtained from a composite of predicted spectra for which the chlorate anions are either both bidentate or both tridentate ligands. In general, we find that the overall accuracy of DFT calculations for prediction of IR spectra is dependent on both functional and basis set, with best agreement achieved using frequencies generated at the B3LYP/6-311+g(3df) level of theory., (Copyright 2009 John Wiley & Sons, Ltd.)

The chemistry of peptide fragmentation by collision-induced dissociation (CID) is currently being reviewed, as a result of observations that the amino acid sequence of peptide fragments can change upon activation. This rearrangement mechanism is thought to be due to a head-to-tail cyclization reaction, where the N-terminal and C-terminal part of the fragment are fused into a macrocycle (= cyclic peptide) structure, thus "losing" the memory of the original sequence. We present a comprehensive study for a series of b fragment ions, from b(2) to b(8), based on the simplest amino acid residue glycine, to investigate the effect of peptide chain length on the appearance of macrocycle fragment structures. The CID product ions are structurally characterized with a range of gas-phase techniques, including isotope labeling, infrared photodissociation spectroscopy, gas-phase hydrogen/deuterium exchange (using CH(3)OD), and computational structure approaches. The combined insights from these results yield compelling evidence that smaller b(n) fragments (n = 2, 3) exclusively adopt oxazolone-type structures, whereas a mixture of oxazolone and macrocycle b fragment structures are formed for midsized b(n) fragments, where n = 4-7. As each of these chemical structures exchanges at different rates, it is possible to approximate the relative abundances using kinetic fits to the H/D exchange data. Under the conditions used here, the "slow"-exchanging macrocycle structure represents approximately 30% of the b ion population for b(6)-b(7), while the "fast"-exchanging oxazolone structure represents the remainder (70%). Intriguingly, for b(8) only the macrocycle structure is identified, which is also consistent with the "slow" kinetic rate in the HDX results. In a control experiment, a protonated cyclic peptide with 6 amino acid residues, cyclo(Gln-Trp-Phe-Gly-Leu-Met), is confirmed not to adopt an oxazolone structure, even upon collisional activation. These results demonstrate that in some cases larger macrocycle structures are surprisingly stable. While more studies are required to establish the general propensity for cyclization in b fragments, the implications from this study are troubling in terms of faulty sequence identification.

Infrared multiple photon dissociation (IRMPD) spectroscopy was used to study formation of b2+ from nicotinyl-glycine-glycine-methyl ester (NicGGOMe). IRMPD shows that NicGGOMe is protonated at the pyridine ring of the nicotinyl group, and more importantly, that b2+ from NicGGOMe is not protonated at the oxazolone ring, as would be expected if the species were generated on the conventional bn+/yn+ oxazolone pathway, but at the pyridine ring instead. IRMPD data support a hypothesis that formation of b2+ from NicGGOMe involves mobilization and transfer of an amide position proton during the fragmentation reaction.

The gas-phase structure of the conjugate base of p-hydroxybenzoic acid (and related compounds) and the influence of the solvent used in its generation by electrospray ionization have recently been under debate. While the phenoxide structure is known to be lower in energy in the gas phase, the carboxylate structure is favored in aqueous solution, fuelling the controversy. Here we probe the structure of this gas-phase anion by IR spectroscopy and show that its structure is determined by the protic or aprotic nature of the solvent, which suggests that it is the solution-phase structure that is transferred to the gas phase.

Tandem mass spectrometry and wavelength-selective infrared photodissociation were used to generate an infrared spectrum of gas-phase triethylphosphate cationized by attachment of K(+). Prominent absorptions were observed in the region of 900 to 1300 cm(-1) that are characteristic of phosphate P=O and P-O-R stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6-31+G(d), 6-311+G(d,p) and 6-311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which in turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations., (Copyright (c) 2009 John Wiley & Sons, Ltd.)

Structures of protonated dipeptides containing N-terminal Gly, Val, Pro, Lys, His, or Arg and C-terminal Arg are investigated with infrared multiple photon dissociation (IRMPD) spectroscopy between 900 and 1850 cm(-1) and theory. The IRMPD spectra clearly indicate that, when Gly, Val, Pro, Lys, or His are N-terminal to Arg, these protonated dipeptides adopt gas-phase structures with a single formal charge site (SCS), whereas ArgArg x H(+) has a salt-bridge (SB) structure in which the C-terminus is deprotonated and two basic sites are protonated. There are only subtle differences in the IRMPD spectra for dipeptides containing Gly, Val, Pro, and Lys. A sharp, intense peak at 1080 cm(-1) is observed for HisArg x H(+) that is attributed to the neutral histidine side chain, an assignment that is confirmed by comparison to the IRMPD spectrum of (HisArg x H(2))(2+). Lowest-energy B3LYP/6-31+G(d,p) structures and energies for the SCS and SB forms of these protonated dipeptides indicate that stability of the SB form relative to the SCS form generally increases with increasing gas-phase basicity of the N-terminal amino acid, but only ArgArg x H(+) is calculated to have a SB ground state at 298 K, in agreement with the results from IRMPD spectroscopy. This is the first direct experimental evidence for a salt-bridge structure in a gaseous protonated peptide, and ArgArg x H(+) is the smallest protonated peptide for which a SB structure has been reported. These results suggest that SB structures should be common for protonated peptides containing at least two arginine residues and may also occur for large protonated peptides or proteins with at least one arginine residue and other basic residues, such as lysine or histidine.

Infrared multiple photon dissociation spectroscopy of gas-phase doubly charged alkaline earth complexes of histidine reveals a transition from dominance of the zwitterion (salt bridge, SB) conformation with Ba2+ to substantial presence of the canonical (charge-solvated, CS) conformation with Ca2+. This result is a clear illustration of the importance of metal-ion size in governing the delicate balance between these two modes of complexation of gas-phase amino acids. The two conformational motifs are clearly distinguished by characteristic spectral features, confirmed by density functional theory simulated IR spectra of the low-energy conformers. As a further illustration of histidine complexation possibilities, the spectrum of the Na+His complex shows purely CS character and emphasizes the greater tendency toward SB character induced by the higher charge in the alkaline earth complexes. Calculation of the complete series of alkaline earth/histidine complexes confirms the increasing stability of the SB conformations relative to CS with increasing metal ion size, as well as showing that among SB conformations the most highly chelated conformation (SB3) is favored for small metals, whereas the most extended conformation (SB1) is favored for large metals. A decomposition of the binding thermochemistry shows that these thermochemical trends versus metal-ion size are due to differences in electrostatic binding energies, with relatively little contribution from the deformation and rearrangement energy costs of distorting the ligand framework.

Infrared multiple photon dissociation action spectra of the binary and ternary gas-phase complexes formed by 15-crown-5 ether with potassium cations (15c5-K(+) and 15c5-K(+)-15c5) are reported. The spectra span the 800-1500 cm(-1) infrared range. Particularly significant differences are found in the position and structure of the CO-stretching band of the two types of complexes. The computational prediction at the DFT-B3LYP/6-31G* level of theory agrees well with the experimental observations, and provides a correlation between the spectral differences and the structural changes associated with the coordination of the ether oxygens with the alkali cation. The 15c5-K(+) complex adopts a pyramidal structure, with the cation lying above the center of mass of the ether ring at a distance similar to its ionic radius. The ternary 15c5-K(+)-15c5 complex features a less tight coordination of the cation and a relative rotation between the backbones of the two crown ethers, which minimizes the intermolecular repulsions between the oxygens.

Electron transfer in K(np)-C(2)Cl(4) collisions, which leads to formation of both Cl(-) and C(2)Cl(4)(-) anions, is investigated as a function of target temperature over the range of 300-650 K. Measurements at high n (n approximately 30) show that the likelihood of Cl(-) production increases rapidly with temperature indicating the presence of a dissociation barrier. The data yield an activation energy of approximately 0.1 eV. A broad distribution of product C(2)Cl(4)(-) lifetimes is observed that extends from microseconds to milliseconds, this distribution moving toward shorter lifetimes as the target temperature is increased. The measured lifetimes are consistent with the predictions of quasiequilibrium theory. Studies at low n (n approximately 14) show a substantial fraction of the product K(+)-Cl(-) and K(+)-C(2)Cl(4)(-) ion pairs is electrostatically bound leading to creation of heavy-Rydberg ion-pair states. Variations in target temperature lead to changes in kinetic energy of relative motion of the reactants that can result in marked changes in the fraction of ion pairs that is bound, especially at low Rydberg atom velocities. In the case of bound K(+)-C(2)Cl(4)(-) ion pairs a few percent subsequently dissociate by the conversion of internal energy in the anion into translational energy of the ion pair. Analysis of the data points to a mean energy conversion of approximately 60-90 meV, much less than the available excess energy of reaction, approximately 0.7 eV.

Gas-phase structures of cationized asparagine (Asn) including complexes with Li(+), Na(+), K(+), Rb(+), Cs(+), and Ba(2+), as well as protonated Asn, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser. Experimental spectra for the alkali metal cation complexes exhibit systematic trends, whereas spectra for Ba(2+)(Asn) and H(+)(Asn) are more distinct. To identify the structures formed experimentally, measured IRMPD spectra are compared to spectra calculated at a B3LYP/6-311+G(d,p) level with several effective core potentials and basis sets evaluated for the heavy metal systems. The dominant conformation ascertained for complexes with the smaller metal cations, Li(+)(Asn) and Na(+)(Asn), is a charge-solvated, tridentate [N,CO,CO] structure that binds the metal cation with the amine group of the amino acid backbone and to the carbonyl oxygen atoms of the backbone and amino acid side chain. For the larger alkali metal cation complexes, K(+)(Asn), Rb(+)(Asn), and Cs(+)(Asn), an additional charge-solvated, tridentate [COOH,CO] structure that binds the metal cation with the two oxygen atoms of the backbone carboxylic acid group and the carbonyl oxygen atom of the Asn side chain may also be present. The Ba(2+)(Asn) spectrum is characteristic of a single charge-solvated [N,CO,CO] conformation, in contrast to Gly, Trp, Arg, Gln, Pro, Ser, Val, and Glu, which all take on a zwitterionic structure when complexed to Ba(2+). In no case do the cationized Asn complexes show definitive evidence of forming a zwitterionic structure in the complexes studied here. For H(+)(Asn), a mixture of two [N,CO] structures, which differ only in the orientation the side chain and are calculated to be nearly identical in energy, explains the experimental spectrum well.

We report on a form of gas-phase anion action spectroscopy based on infrared multiple photon electron detachment and subsequent capture of the free electrons by a neutral electron scavenger in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. This method allows one to obtain background-free spectra of strongly bound anions, for which no dissociation channels are observed. The first gas-phase spectra of acetate and propionate are presented using SF(6) as electron scavenger and a free electron laser as source of intense and tunable infrared radiation. To validate the method, we compare infrared spectra obtained through multiple photon electron detachment/attachment and multiple photon dissociation for the benzoate anion. In addition, different electron acceptors are used, comparing both associative and dissociative electron capture. The relative energies of dissociation (by CO(2) loss) and electron detachment are investigated for all three anions by DFT and CCSD(T) methods. DFT calculations are also employed to predict vibrational frequencies, which provide a good fit to the infrared spectra observed. The frequencies of the symmetric and antisymmetric carboxylate stretching modes for the aliphatic carboxylates are compared to those previously observed in condensed-phase IR spectra and to those reported for gas-phase benzoate, showing a strong influence of the solution environment and a slight substituent effect on the antisymmetric stretch.

1,2-Dihydronaphthalene (DHN) has been studied by matrix isolation infrared absorption spectroscopy, multiphoton infrared photodissociation (IRMPD) action spectroscopy, and density functional theory calculations. Formed by electrospray ionization, protonated 1,2-dihydronapthalene was injected into a Fourier transform ion cyclotron resonance mass spectrometer coupled to an infrared-tunable free electron laser and its IRMPD spectrum recorded. Multiphoton infrared irradiation of the protonated parent (m/z 131) yields two dissociation products, one with m/z 129 and the other with m/z 91. Results from density functional theory calculations (B3LYP/6-31++G(d,p)) were compared to the low-temperature matrix isolation infrared spectrum of neutral DHN, with excellent results. Calculations reveal that the most probable site of protonation is the 3-position, producing the trihydronaphthalene (THN) cation, 1,2,3-THN(+). The observed IRMPD spectrum of vapor-phase protonated parent matches well with that computed for 1,2,3-THN(+). Extensive B3LYP/6-31G(d,p) calculations of the potential energy surface of 1,2,3-THN(+) have been performed and provide insight into the mechanism of the two-channel photodissociation. These results provide support for a new model of the formation of H(2) in the interstellar medium. This model involves hydrogenation of a PAH cation to produce one or more aliphatic hydrogen-bearing carbons on the PAH framework, followed by photolytic formation and ejection of H(2).

Gas-phase infrared multiple photon dissociation (IRMPD) spectra have been recorded for the conjugate bases of a series of amino acids (Asp, Cys, Glu, Phe, Ser, Trp, Tyr). The spectra are dominated by strong symmetric and antisymmetric carboxylate stretching modes around 1300 and 1600 cm(-1), respectively. Comparison of the experimental spectra with spectra calculated at the DFT level suggests a carboxylate structure for all species investigated, which is in contrast with what has recently been suggested in this journal for deprotonated cysteine [J. Am. Chem. Soc. 2007, 129, 5403-5407]. In addition, the IR spectrum of the conjugate base of tyrosine is also unambiguously that of a carboxylate ion and not that of a phenoxide ion. In sharp contrast with the conjugate bases of other amino acids investigated here, the aspartate and glutamate anions show very broad, hardly resolved spectral features. We present qualitative experimental evidence indicating that this can be attributed to the formation of a proton bridge between the backbone and side chain carboxylate groups. The large amplitude motion of this shared proton, coupling to virtually all other vibrational modes, causes extensive spectral broadening.

Proton-bound dimers consisting of valine and basic primary and secondary amines of varying gas-phase basicity (GB) were investigated using infrared multiple photon dissociation (IRMPD) spectroscopy between 800 and 3700 cm(-1), collisionally activated dissociation, and theory. The low-energy dissociation of these dimers results in a sharp transition from formation of primarily protonated valine to protonated base for dimers with ethylamine and propylamine, respectively, from which a GB of approximately 880 kJ/mol is deduced for valine, a value that is slightly higher than previously reported. The IRMPD spectra clearly indicate that, for bases with GB values within 20 kJ/mol of that of valine, the base coordinates to the N-terminus of a nonzwitterionic form of valine. In contrast, calculations indicate that valine is zwitterionic for complexes where the base is less basic. For bases with GB values at least 20 kJ/mol greater than that of valine, the spectra indicate a transition in structure, and for diethylamine (DeltaGB = 40 kJ/mol), the dominant structure is one in which the base coordinates to the carbonyl oxygen of a nonzwitterionic form of valine and the carboxylic acid donates an intramolecular hydrogen bond to the N-terminus. These results are consistent with the destabilization of the N-terminally coordinated structure due to the increasing difference in proton affinities of the constituent molecules and the increasing importance of a stabililizing hydrogen bond formed in the C-terminally coordinated structure. Even when the GB of the base is 40 kJ/mol higher than that of valine, the form of the amino acid is nonzwitterionic, indicating that careful application of the kinetic method should provide reliable information about the basicity of valine and other aliphatic amino acids.